Sorry, I'm not sure the size of my 2008 R25 yanmar 4jh4hte 110hp engine. I did replace the packing in the stuffing box with GFO dripless packing. It is similar to the regular packing but you first put it in ( 3 strips) and run the boat a few times and slowly tighten the stuffing box about a 1/4 inch till it stops dripping. I did this about 4 years ago and just readjusted it the other day. I also have a temperature laser and I check it while running. I was told that a Temp. under 105 degrees is alright. Mine runs about 85 to 90 even in the hot summer when the water is very warm down here in SE Virginia. I have never had a problem with it. I readjusted it since I thought the stuffing nut might have loosened up a tiny bit.
I'll check the shaft diameter and let you know. Actually I think it might be 1 1/4.
jimbeam